No I wouldn't say the source of all knowledge, but ultimately knowledge must be indicated in evidence. Science is a method and an enterprise that specializes at progressively converging to an underlying truth. Science is a method of discovering the nature of nature itself using empirical evidence and experimentation. Science is based on methodological naturalism, which states that only natural causes are to be considered as explanations, in contradistinction to philosophical naturalism which asserts that only natural things exist (and that the supernatural does not exist). Since there is no way to demonstrate and confirm supernatural causation, entities which are said to inhabit the supernatural realm are simply not considered in science. The means by which science is executed is known as the scientific method. Science has proven to be the only consistently reliable method of defining reality. Science, by definition, cannot consider supernatural explanations as they are simply unverifiable assertions. Supernatural explanations have yet to provide any reliable, verifiable information about reality, and hence remain a matter of faith. If a supernatural claim does contain scientifically testable assertions, then those assertions may be tested to see if they hold up in nature.

The fact that science doesn't currently have all the answers to every question about life, the universe, and everything certainly doesn't mean that science as a whole is unreliable. Two centuries ago science had very little information (and in many cases none at all) about things like quantum mechanics, dark matter, the age of the universe, etc. However, nowadays we know much more simply because science is constantly progressing. Indeed, the rate of scientific progression seems to increase the more we learn.

Methodological naturalism is the stance that only natural causes will be considered in explanations. This is in contrast to philosophical naturalism, the stance that only natural things exist.

For example, consider an auto mechanic trying to figure out why a car is making a funny noise. He may hypothesize that a part is worn out, or that a coupling is loose, that some parts have come out of alignment, etc. But he probably won't seriously consider supernatural causes such as ghosts, gremlins, or demons. This mechanic is using methodological naturalism. If this mechanic is also a theist, then he uses methodological naturalism in his job, but does not subscribe to philosophical naturalism.

"Once miracles are admitted, every scientific explanation is out of the question."

Science uses methodological naturalism. That is, explanations that include supernatural elements, e.g., that atoms are held together by tiny spirits, are not considered scientific.

Some critics, notably Intelligent design proponents, charge that this is an arbitrary restriction that blocks exploration of potentially fruitful areas of research.

However, science is eminently practical. The reason scientists don't consider supernatural explanations is that there is no way to test them to see whether they're correct. In the example above, an auto mechanic may hypothesize that a problem was caused by evil spirits, but there is no reliable way to either confirm or disconfirm this hypothesis. To put it bluntly, the reason that scientists don't consider supernatural explanations is that they don't work.

Note that it is conceivable that someone might some day come up with a testable explanation for some phenomenon that involves a supernatural entity. If a genuine miracle ever occurred, this rule would have to be revisited. In the meantime, given supernaturalism's track record, it seems safe for scientists to avoid it.

Naturalism ignores God
"The reason the theory of evolution is so controversial is that it is the main scientific prop for scientific naturalism. Students first learn that "evolution is a fact," and then they gradually learn more and more about what that "fact" means. It means that all living things are the product of mindless material forces such as chemical laws, natural selection, and random variation. So God is totally out of the picture, and humans (like everything else) are the accidental product of a purposeless universe. Do you wonder why a lot of people suspect that these claims go far beyond the available evidence?"

Naturalism ignores supernatural explanations. If evidence of God existed, he would be considered to be "within nature" for the purpose of explanations. By this argument, the apologist implicitly admits there is no evidence for God.

Methodological naturalism is the foundation for science. It states that people don't currently possess the capability of investigating the supernatural, and so science confines its methodology to the realm of this type of naturalism. It is not a pronouncement that the supernatural doesn't exist. It is an acknowledgment that we cannot test for and confirm the supernatural. For everything that we have got a successful explanation for, the answer has been natural.